Rick Ankiel singled in Washington's third run in the ninth with two outs but was later thrown out trying to steal second.
Gio Gonzalez (2-0) allowed two hits and struck out six in six innings for the victory. Henry Rodriguez was credited with his fifth save of the season.
Clayton Richard (1-2) took the loss, which ended San Diego's two-game winning streak. Richard gave up two runs on three hits and walked five in 6 1/3 innings.
San Diego scored its only run in the bottom half of the seventh when Andy Parrino singled with two runners aboard.